+;;; Module:      biotool.core
+;;; Description: Reads one or more FASTA files and computes various
+;;;              simple statistics about them. Intended as an example
+;;;              bioinformatics command line tool 
+;;; Copyright:   (c) Bernie Pope, 2017 
+;;; License:     MIT 
+;;; Maintainer:  bjpope@unimelb.edu.au
+;;; Stability:   stable 
+;;; Portability: POSIX
+
+;;; The main parts of the program are:
+;;; 1. Parse command line arguments. 
+;;; 2. Process each FASTA file in sequence
+;;; 3. Pretty print output for each file. 
+;;;
+;;; If no FASTA filenames are specified on the command line then the program
+;;; will try to read a FASTA file from standard input.
+
 (ns biotool.core
   (:require [clj-biosequence.core :as bs]
             [clojure.string :as string]

      (process-stdin minlen)
      (doseq [file files]
         (process-fasta-file minlen file))))

(defn usage [options-summary]
  (->> ["Print fasta stats"

        options-summary]
       (string/join \newline)))


(defn error-msg [errors]
  (str "The following errors occurred while parsing your command:\n\n"
       (string/join \newline errors)))


(defn exit [status msg]
  (println msg)
  (System/exit status))


(def default-minlen 0)


(def cli-options
  [[nil "--minlen N" "Minimum length sequence to include in stats"
